4EB1

Hyperstable in-frame insertion variant of antithrombin

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history. 

Literature

Type II antithrombin deficiency caused by a large in-frame insertion: structural, functional and pathological relevance.

Martinez-Martinez, I., Johnson, D.J., Yamasaki, M., Navarro-Fernandez, J., Ordonez, A., Vicente, V., Huntington, J.A., Corral, J.

(2012) J.Thromb.Haemost. 10: 1859-1866

  • DOI: 10.1111/j.1538-7836.2012.04839.x

  • PubMed Abstract: 

    • The metastable native conformation of serpins is required for their protease inhibition mechanism, but also renders them vulnerable to missense mutations that promote protein misfolding with pathological consequences.

    The metastable native conformation of serpins is required for their protease inhibition mechanism, but also renders them vulnerable to missense mutations that promote protein misfolding with pathological consequences.

    Organizational Affiliation: 

    Centro Regional de Hemodonación, University of Murcia, Regional Campus of International Excellence Campus Mare Nostrum, Murcia, Spain.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Antithrombin-III
I
440Homo sapiensMutation(s): 1 
Gene Names: SERPINC1 (AT3)
Find proteins for P01008 (Homo sapiens)
Go to Gene View: SERPINC1
Go to UniProtKB:  P01008
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Antithrombin-III
L
432Homo sapiensMutation(s): 0 
Gene Names: SERPINC1 (AT3)
Find proteins for P01008 (Homo sapiens)
Go to Gene View: SERPINC1
Go to UniProtKB:  P01008
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download SDF File 
Download CCD File 
I, L
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.255 
  • R-Value Work: 0.198 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 69.750α = 90.00
b = 101.750β = 105.42
c = 88.810γ = 90.00
Software Package:
Software NamePurpose
PHASERphasing
SCALAdata scaling
REFMACrefinement
MOSFLMdata reduction
HKL-2000data collection

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2012-07-18
    Type: Initial release
  • Version 1.1: 2012-09-19
    Type: Database references
  • Version 1.2: 2017-07-26
    Type: Refinement description, Source and taxonomy